Limits to the number of citations allowed in an article are common in academic writing, and journals often differ in the number of references allowed. It can often be hard to remember, when revising an article, which references in a document were most important and which could be removed if necessary. The ability to rate references within a document (i.e. "essential", "important", "optional" etc.) would be really helpful. Maybe the tags within the document could be colour-coded?

By the way, thanks for the 1.1.4 update! I am finding Manuscripts to be far more stable and enjoyable to use, this is a real improvement where it matters.

Come to think of it, a continuously-updated reference count next to the word count would be a really neat addition too - it's a real pain to have to keep switching back to Vancouver style to count references!